| typedef std::vector<SequenceIOHandlerFactoryBasePtr> AlignmentIOFList |
Definition at line 41 of file io_manager.hh.
Definition at line 52 of file clustal_io_handler.hh.
Definition at line 109 of file entity_io_crd_handler.hh.
| typedef boost::shared_ptr< EntityIOHandlerFactoryBase > EntityIOHandlerFactoryBaseP |
Definition at line 77 of file entity_io_handler.hh.
| typedef boost::shared_ptr< EntityIOHandler > EntityIOHandlerP |
Definition at line 63 of file entity_io_handler.hh.
| typedef std::vector<EntityIOHandlerFactoryBaseP> EntityIOHFList |
Definition at line 40 of file io_manager.hh.
Definition at line 83 of file entity_io_mae_handler.hh.
Definition at line 54 of file entity_io_mmcif_handler.hh.
Definition at line 55 of file entity_io_pdb_handler.hh.
Definition at line 109 of file entity_io_pqr_handler.hh.
Definition at line 49 of file entity_io_sdf_handler.hh.
Definition at line 53 of file fasta_io_handler.hh.
Definition at line 48 of file hhm_io_handler.hh.
Definition at line 61 of file map_io_mrc_handler.hh.
Definition at line 80 of file map_io_dat_handler.hh.
Definition at line 71 of file map_io_df3_handler.hh.
Definition at line 59 of file map_io_dm3_handler.hh.
Definition at line 74 of file map_io_dx_handler.hh.
| typedef std::vector<MapIOHandlerFactoryBasePtr> MapIOFList |
Definition at line 46 of file io_manager.hh.
| typedef boost::shared_ptr< MapIOHandlerFactoryBase > MapIOHandlerFactoryBasePtr |
Definition at line 57 of file map_io_handler.hh.
| typedef boost::shared_ptr< MapIOHandler > MapIOHandlerPtr |
Definition at line 42 of file map_io_handler.hh.
Definition at line 74 of file map_io_ipl_handler.hh.
Definition at line 57 of file map_io_jpk_handler.hh.
Definition at line 94 of file map_io_mrc_handler.hh.
Definition at line 67 of file map_io_nanoscope_handler.hh.
Definition at line 65 of file map_io_png_handler.hh.
Definition at line 64 of file map_io_situs_handler.hh.
Definition at line 77 of file map_io_spi_handler.hh.
Definition at line 120 of file map_io_tiff_handler.hh.
| typedef boost::shared_ptr< MMCifInfoStructRef > MMCifInfoStructRefPtr |
Definition at line 769 of file mmcif_info.hh.
| typedef std::vector< MMCifInfoStructRefPtr > MMCifInfoStructRefs |
Definition at line 776 of file mmcif_info.hh.
| typedef boost::shared_ptr< MMCifInfoStructRefSeqDif > MMCifInfoStructRefSeqDifPtr |
Definition at line 774 of file mmcif_info.hh.
| typedef std::vector< MMCifInfoStructRefSeqDifPtr > MMCifInfoStructRefSeqDifs |
Definition at line 778 of file mmcif_info.hh.
| typedef boost::shared_ptr< MMCifInfoStructRefSeq > MMCifInfoStructRefSeqPtr |
Definition at line 773 of file mmcif_info.hh.
| typedef std::vector< MMCifInfoStructRefSeqPtr > MMCifInfoStructRefSeqs |
Definition at line 777 of file mmcif_info.hh.
| typedef boost::shared_ptr< MMCifInfoTransOp > MMCifInfoTransOpPtr |
Definition at line 246 of file mmcif_info.hh.
Definition at line 53 of file pir_io_handler.hh.
| typedef std::vector<ProfileIOHandlerFactoryBasePtr> ProfileIOFList |
Definition at line 42 of file io_manager.hh.
| typedef boost::shared_ptr< ProfileIOHandlerFactoryBase > ProfileIOHandlerFactoryBasePtr |
Definition at line 63 of file profile_io_handler.hh.
| typedef boost::shared_ptr< ProfileIOHandler > ProfileIOHandlerPtr |
Definition at line 48 of file profile_io_handler.hh.
Definition at line 53 of file promod_io_handler.hh.
Definition at line 50 of file pssm_io_handler.hh.
| typedef boost::shared_ptr< SequenceIOHandlerFactoryBase > SequenceIOHandlerFactoryBasePtr |
Definition at line 67 of file sequence_io_handler.hh.
| typedef boost::shared_ptr< SequenceIOHandler > SequenceIOHandlerPtr |
Definition at line 51 of file sequence_io_handler.hh.
| typedef std::vector<SurfaceIOHandlerFactoryBasePtr> SurfaceIOFList |
Definition at line 43 of file io_manager.hh.
| typedef boost::shared_ptr< SurfaceIOHandlerFactoryBase > SurfaceIOHandlerFactoryBasePtr |
Definition at line 48 of file surface_io_handler.hh.
| typedef boost::shared_ptr< SurfaceIOHandler > SurfaceIOHandlerPtr |
Definition at line 36 of file surface_io_handler.hh.
Definition at line 41 of file surface_io_msms_handler.hh.
| enum Endianess |
Definition at line 28 of file convert.hh.
| enum Format |
Definition at line 68 of file image_format.hh.
| enum Format |
Definition at line 68 of file image_format.hh.
| enum LoopType |
Definition at line 34 of file chemdict_parser.hh.
| enum LoopType |
Definition at line 34 of file chemdict_parser.hh.
| enum StarDiagType |
Definition at line 38 of file star_parser.hh.
| enum StarDiagType |
Definition at line 38 of file star_parser.hh.
| enum Subformat |
| MRC_OLD_FORMAT | |
| MRC_NEW_FORMAT | |
| MRC_AUTO_FORMAT | |
| MRC_OLD_FORMAT | |
| MRC_NEW_FORMAT | |
| MRC_AUTO_FORMAT |
Definition at line 73 of file image_format.hh.
| enum Subformat |
| MRC_OLD_FORMAT | |
| MRC_NEW_FORMAT | |
| MRC_AUTO_FORMAT | |
| MRC_OLD_FORMAT | |
| MRC_NEW_FORMAT | |
| MRC_AUTO_FORMAT |
Definition at line 73 of file image_format.hh.
| seq::AlignmentHandle DLLIMPORT AlignmentFromStream | ( | std::istream & | stream, | |
| const String & | format | |||
| ) |
| seq::AlignmentHandle DLLIMPORT AlignmentFromString | ( | const String & | data, | |
| const String & | format | |||
| ) |
| String DLLIMPORT EntityToPDBString | ( | const mol::EntityView & | ent, | |
| const IOProfile & | profile = IOProfile() | |||
| ) |
| String DLLIMPORT EntityToPDBString | ( | const mol::EntityHandle & | ent, | |
| const IOProfile & | profile = IOProfile() | |||
| ) |
| seq::AlignmentHandle DLLIMPORT LoadAlignment | ( | const String & | file_name, | |
| const String & | format = "auto" | |||
| ) |
| def ost::io::LoadCHARMMTraj | ( | crd, | ||
dcd_file = None, |
||||
profile = 'CHARMM', |
||||
lazy_load = False, |
||||
stride = 1, |
||||
dialect = None, |
||||
detect_swap = True, |
||||
swap_bytes = False | ||||
| ) |
Load CHARMM trajectory file.
:param crd: EntityHandle or filename of the (PDB) file containing the
structure. The structure must have the same number of atoms as the
trajectory
:param dcd_file: The filename of the DCD file. If not set, and crd is a
string, the filename is set to the <crd>.dcd
:param layz_load: Whether the trajectory should be loaded on demand. Instead
of loading the complete trajectory into memory, the trajectory frames are
loaded from disk when requested.
:param stride: The spacing of the frames to load. When set to 2, for example,
every second frame is loaded from the trajectory. By default, every frame
is loaded.
:param dialect: The dialect for the PDB file to use. See :func:`LoadPDB`. If
set, overrides the value of the profile
:param profile: The IO profile to use for loading the PDB file. See
:doc:`profile`.
:param detect_swap: if True (the default), then automatic detection of endianess
is attempted, otherwise the swap_bytes parameter is used
:param swap_bytes: is detect_swap is False, this flag determines whether bytes
are swapped upon loading or not
Definition at line 223 of file __init__.py.
| mol::CoordGroupHandle DLLIMPORT LoadCHARMMTraj | ( | const mol::EntityHandle & | ent, | |
| const String & | trj_filename, | |||
| unsigned int | stride = 1, |
|||
| bool | lazy_load = false, |
|||
| bool | detect_swap = true, |
|||
| bool | byte_swap = false | |||
| ) |
import a CHARMM trajectory in dcd format with an existing entity requires the existing entity and the trajectory file - obviously the atom layout of the entity must match the trajectory file
| mol::EntityHandle DLLIMPORT LoadCRD | ( | const String & | file_name | ) |
| DLLIMPORT mol::EntityHandle LoadEntity | ( | const String & | filename, | |
| int | flag = 0 | |||
| ) |
| DLLEXPORT_OST_IO img::ImageHandle LoadImage | ( | const boost::filesystem::path & | loc, | |
| const ImageFormatBase & | formatstruct | |||
| ) |
Function that loads an image from a file with a specific format.
This function reads an image file from disk and transfers the data into memory The function assumes that the file has the specified format
| DLLEXPORT_OST_IO img::ImageHandle LoadImage | ( | const boost::filesystem::path & | loc | ) |
Function that loads an image from a file.
This function reads an image file from disk and transfers the data into memory The function automatically determines the file format by looking at the filename extension. In case the extension is not available, the content of the file will be examined. This analysis will be sufficient to determine the format type for many files. In case the file format cannot be determined, the function will throw an error.
| def ost::io::LoadImageList | ( | files | ) |
Definition at line 214 of file __init__.py.
| mol::EntityHandle DLLIMPORT LoadMAE | ( | const String & | file_name | ) |
| DLLIMPORT mol::SurfaceHandle LoadManagedSurface | ( | const String & | name, | |
| const String & | filename, | |||
| const String & | type = "auto" | |||
| ) |
| DLLEXPORT_OST_IO img::MapHandle LoadMap | ( | const boost::filesystem::path & | loc, | |
| const ImageFormatBase & | formatstruct | |||
| ) |
Alias for the equivalent LoadImage function.
| DLLEXPORT_OST_IO img::MapHandle LoadMap | ( | const boost::filesystem::path & | loc | ) |
Alias for the equivalent LoadImage function.
| def ost::io::LoadMMCIF | ( | filename, | ||
restrict_chains = "", |
||||
fault_tolerant = None, |
||||
calpha_only = None, |
||||
profile = 'DEFAULT', |
||||
remote = False, |
||||
seqres = False, |
||||
info = False | ||||
| ) |
Load MMCIF file from disk and return one or more entities. Several options
allow to customize the exact behaviour of the MMCIF import. For more
information on these options, see :doc:`profile`.
Residues are flagged as ligand if they are mentioned in a HET record.
:param restrict_chains: If not an empty string, only chains listed in the
string will be imported.
:param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides
the value of :attr:`IOProfile.fault_tolerant`.
:param remote: If set to True, the method tries to load the pdb from the
remote pdb repository www.pdb.org. The filename is then interpreted as the
pdb id.
:rtype: :class:`~ost.mol.EntityHandle`.
:param seqres: Whether to read SEQRES records. If set to True, the loaded
entity and seqres entry will be returned as second item.
:param info: Whether to return an info container with the other output.
Returns a :class:`MMCifInfo` object as last item.
:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous
or non-existent file.
Definition at line 259 of file __init__.py.
| def ost::io::LoadPDB | ( | filename, | ||
restrict_chains = "", |
||||
no_hetatms = None, |
||||
fault_tolerant = None, |
||||
load_multi = False, |
||||
quack_mode = None, |
||||
join_spread_atom_records = None, |
||||
calpha_only = None, |
||||
profile = 'DEFAULT', |
||||
remote = False, |
||||
dialect = None, |
||||
seqres = False, |
||||
bond_feasibility_check = None | ||||
| ) |
Load PDB file from disk and return one or more entities. Several options
allow to customize the exact behaviour of the PDB import. For more information
on these options, see :doc:`profile`.
Residues are flagged as ligand if they are mentioned in a HET record.
:param restrict_chains: If not an empty string, only chains listed in the
string will be imported.
:param fault_tolerant: Enable/disable fault-tolerant import. If set, overrides
the value of :attr:`IOProfile.fault_tolerant`.
:param no_hetatms: If set to True, HETATM records will be ignored. Overrides
the value of :attr:`IOProfile.no_hetatms`
:param load_multi: If set to True, a list of entities will be returned instead
of only the first. This is useful when dealing with multi-PDB files.
:param join_spread_atom_records: If set, overrides the value of
:attr:`IOProfile.join_spread_atom_records`.
:param remote: If set to True, the method tries to load the pdb from the
remote pdb repository www.pdb.org. The filename is then interpreted as the
pdb id.
:rtype: :class:`~ost.mol.EntityHandle` or a list thereof if `load_multi` is
True.
:param dialect: Specifies the particular dialect to use. If set, overrides
the value of :attr:`IOProfile.dialect`
:param seqres: Whether to read SEQRES records. If set to True, the loaded
entity and seqres entry will be returned as a tuple.
:type dialect: :class:`str`
:raises: :exc:`~ost.io.IOException` if the import fails due to an erroneous or
inexistent file
Definition at line 65 of file __init__.py.
| mol::EntityHandle DLLIMPORT LoadPQR | ( | const String & | file_name | ) |
| mol::EntityHandle DLLIMPORT LoadSDF | ( | const String & | file_name | ) |
| seq::SequenceHandle DLLIMPORT LoadSequence | ( | const String & | file_name, | |
| const String & | format = "auto" | |||
| ) |
| seq::SequenceList DLLIMPORT LoadSequenceList | ( | const String & | file_name, | |
| const String & | format = "auto" | |||
| ) |
| seq::ProfileHandlePtr DLLIMPORT LoadSequenceProfile | ( | const String & | file_name, | |
| const String & | format = "auto" | |||
| ) |
| DLLIMPORT mol::SurfaceHandle LoadSurface | ( | const String & | filename, | |
| const String & | type = "auto" | |||
| ) |
| std::ostream & operator<< | ( | std::ostream & | stream, | |
| const IOProfile & | p | |||
| ) | [inline] |
Definition at line 61 of file io_profile.hh.
| std::ostream& ost::io::operator<< | ( | std::ostream & | stream, | |
| const FormattedLine & | line | |||
| ) | [inline] |
Definition at line 229 of file formatted_line.hh.
| mol::EntityHandle DLLIMPORT PDBStringToEntity | ( | const String & | pdb, | |
| const IOProfile & | profile = IOProfile() | |||
| ) |
| void ost::io::RawSerialize | ( | BinaryDataSource & | sink, | |
| char * | value, | |||
| size_t | size | |||
| ) | [inline] |
Definition at line 87 of file binary_data_source.hh.
| void ost::io::RawSerialize | ( | BinaryDataSink & | sink, | |
| char * | value, | |||
| size_t | size | |||
| ) | [inline] |
Definition at line 87 of file binary_data_sink.hh.
| void DLLIMPORT SaveAlignment | ( | const seq::AlignmentHandle & | msa, | |
| const String & | filename, | |||
| const String & | format = "auto" | |||
| ) |
| void DLLIMPORT SaveCHARMMTraj | ( | const mol::CoordGroupHandle & | coord_group, | |
| const String & | pdb_filename, | |||
| const String & | dcd_filename, | |||
| unsigned int | stride = 1, |
|||
| const IOProfile & | profile = IOProfile() | |||
| ) |
export coord group as PDB file and DCD trajectory if the pdb filename is an empty string, it won't be exported the optional stride parameter will cause every nth frame to be exported
| void DLLIMPORT SaveEntity | ( | const mol::EntityView & | en, | |
| const String & | filename, | |||
| const String & | format = "auto" | |||
| ) |
Save entity view.
This method provides a convenient way to save only a certain part of an entity, i.e. to filter out water and ligands or to create a backbone-only model.
| en | is the entity view to be saved. | |
| filename | is the output filename | |
| format | specifies what output format is used for export. If set to auto the format is deduced from the file extension |
| void DLLIMPORT SaveEntity | ( | const mol::EntityHandle & | en, | |
| const String & | filename, | |||
| const String & | format = "auto" | |||
| ) |
Save entity handle.
| en | is the entity to be saved | |
| filename | is the output filename | |
| format | specifies what output format is used for export. If set to auto the format is deduced from the file extension |
| DLLEXPORT_OST_IO void SaveImage | ( | const img::ImageHandle & | image, | |
| const boost::filesystem::path & | loc, | |||
| const ImageFormatBase & | formatstruct | |||
| ) |
Function that saves an image to a file using a specified format.
This function saves an image on disk using the format specified in the function call
| DLLEXPORT_OST_IO void SaveImage | ( | const img::ImageHandle & | image, | |
| const boost::filesystem::path & | loc | |||
| ) |
Function that saves an image to a file.
This function saves an image on disk. The function automatically determines the file format by looking at the filename extension. In case the extension is not availabel, the function will throw an error
| DLLEXPORT_OST_IO void SaveMap | ( | const img::ImageHandle & | image, | |
| const boost::filesystem::path & | loc, | |||
| const ImageFormatBase & | formatstruct | |||
| ) |
Alias for the equivalent SaveImage function.
| DLLEXPORT_OST_IO void SaveMap | ( | const img::ImageHandle & | image, | |
| const boost::filesystem::path & | loc | |||
| ) |
Alias for the equivalent SaveImage function.
| def ost::io::SavePDB | ( | models, | ||
| filename, | ||||
dialect = None, |
||||
pqr = False, |
||||
profile = 'DEFAULT' | ||||
| ) |
Save entity or list of entities to disk. If a list of entities is supplied the PDB file will be saved as a multi PDB file. Each of the entities is wrapped into a MODEL/ENDMDL pair. If the atom number exceeds 99999, '*****' is used. :param models: The entity or list of entities (handles or views) to be saved :param filename: The filename :type filename: string
Definition at line 176 of file __init__.py.
| void DLLIMPORT SaveSequence | ( | const seq::ConstSequenceHandle & | sequence, | |
| const String & | filename, | |||
| const String & | format = "auto" | |||
| ) |
| void DLLIMPORT SaveSequenceList | ( | const seq::ConstSequenceList & | seq_list, | |
| const String & | filename, | |||
| const String & | format = "auto" | |||
| ) |
| seq::SequenceHandle DLLIMPORT SequenceFromStream | ( | std::istream & | stream, | |
| const String & | format | |||
| ) |
| seq::SequenceHandle DLLIMPORT SequenceFromString | ( | const String & | data, | |
| const String & | format | |||
| ) |
| seq::SequenceList DLLIMPORT SequenceListFromStream | ( | std::istream & | stream, | |
| const String & | format | |||
| ) |
| seq::SequenceList DLLIMPORT SequenceListFromString | ( | const String & | data, | |
| const String & | format | |||
| ) |
| String DLLIMPORT SequenceListToString | ( | const seq::ConstSequenceList & | seq_list, | |
| const String & | format | |||
| ) |
| String DLLIMPORT SequenceToString | ( | const seq::ConstSequenceHandle & | sequence, | |
| const String & | format = "auto" | |||
| ) |
| void ost::io::Serialize | ( | BinaryDataSource & | source, | |
| std::map< K, V > & | value | |||
| ) | [inline] |
Definition at line 72 of file container_serialization.hh.
| void ost::io::Serialize | ( | BinaryDataSink & | sink, | |
| const std::map< K, V > & | value | |||
| ) | [inline] |
Definition at line 62 of file container_serialization.hh.
| void ost::io::Serialize | ( | BinaryDataSource & | source, | |
| std::vector< T > & | value | |||
| ) | [inline] |
Definition at line 46 of file container_serialization.hh.
| void ost::io::Serialize | ( | BinaryDataSink & | sink, | |
| const std::vector< T > & | value | |||
| ) | [inline] |
Definition at line 32 of file container_serialization.hh.
| void ost::io::Serialize | ( | BinaryDataSource & | source, | |
| String & | str | |||
| ) | [inline] |
Definition at line 93 of file binary_data_source.hh.
| void ost::io::Serialize | ( | BinaryDataSource & | source, | |
| T & | value | |||
| ) | [inline] |
Definition at line 80 of file binary_data_source.hh.
| void ost::io::Serialize | ( | BinaryDataSink & | sink, | |
| const String & | str | |||
| ) | [inline] |
Definition at line 92 of file binary_data_sink.hh.
| void ost::io::Serialize | ( | BinaryDataSink & | sink, | |
| const T & | value | |||
| ) | [inline] |
Definition at line 79 of file binary_data_sink.hh.
| void swap_buf | ( | T * | p, | |
| int | n | |||
| ) | [inline] |
Definition at line 55 of file swap_util.hh.
| void ost::io::swap_double | ( | double * | p, | |
| int | n | |||
| ) | [inline] |
Definition at line 49 of file swap_util.hh.
| void ost::io::swap_float | ( | float * | p, | |
| int | n | |||
| ) | [inline] |
Definition at line 47 of file swap_util.hh.
| void ost::io::swap_int | ( | int * | p, | |
| int | n | |||
| ) | [inline] |
Definition at line 43 of file swap_util.hh.
| void ost::io::swap_long | ( | long * | p, | |
| int | n | |||
| ) | [inline] |
Definition at line 51 of file swap_util.hh.
| void ost::io::swap_short | ( | short int * | p, | |
| short int | n | |||
| ) | [inline] |
Definition at line 39 of file swap_util.hh.
| void ost::io::swap_uint | ( | uint * | p, | |
| int | n | |||
| ) | [inline] |
Definition at line 45 of file swap_util.hh.
| void ost::io::swap_ushort | ( | unsigned short int * | p, | |
| short int | n | |||
| ) | [inline] |
Definition at line 41 of file swap_util.hh.
| tuple processor = conop.RuleBasedProcessor(conop.GetDefaultLib()) |
Definition at line 48 of file __init__.py.
| tuple profiles = None |
Definition at line 24 of file __init__.py.
| tuple quack_mode = False,processorprocessor.Copy() |
Definition at line 52 of file __init__.py.
1.6.1